shinySISPA: A web tool for defining sample groups using gene sets from multiple-omics data

As opposed to genome-wide testing of several hundreds of thousands of genes on very few samples, gene panels target as few as tens of genes and enable the simultaneous testing of many samples. For example, some cancer gene panels test for 50 genes that can affect tumor growth and potentially identify treatment options directed against the genetic mutation. The increasing popularity of gene panel testing has spurred the technological development of panels that test for diverse data types such as expression and mutation. Once samples are tested, there is the desire to examine clinical associations based on the panel and for this purpose, one would like to identify, among the samples tested, which show support for a molecular profile (e.g., presence of mutation with increased expression) versus those samples that do not among the genes tested. With user-specified molecular profile of interest, and gene panel data matrices (e.g., gene expression, variants, etc.) that define the profile, shinySISPA (Sample Integrated Set Profile Analysis) is a web-based shiny tool to define two sample groups with and without profile support based on our previously published method from which clinical associations may be readily examined. The shinySISPA can be accessed from http://shinygispa.winship.emory.edu/shinySISPA/.